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- PDB-4rhw: Crystal structure of Apaf-1 CARD and caspase-9 CARD complex -

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Basic information

Entry
Database: PDB / ID: 4rhw
TitleCrystal structure of Apaf-1 CARD and caspase-9 CARD complex
Components
  • Apoptotic protease-activating factor 1
  • Caspase-9
KeywordsAPOPTOSIS / death domain superfamily
Function / homology
Function and homology information


caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion ...caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / epithelial cell apoptotic process / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / platelet formation / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / Constitutive Signaling by AKT1 E17K in Cancer / cysteine-type endopeptidase activator activity involved in apoptotic process / protein maturation / enzyme activator activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / signal transduction in response to DNA damage / forebrain development / positive regulation of apoptotic signaling pathway / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / response to nutrient / kidney development / neural tube closure / response to ischemia / ADP binding / NOD1/2 Signaling Pathway / protein processing / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / nervous system development / peptidase activity / neuron apoptotic process / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / response to lipopolysaccharide / cell differentiation / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / nucleotide binding / apoptotic process / DNA damage response / Neutrophil degranulation / protein kinase binding / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CASP9, CARD domain / Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / Death Domain, Fas / Death Domain, Fas ...CASP9, CARD domain / Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / Death Domain, Fas / Death Domain, Fas / NB-ARC / NB-ARC domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptotic protease-activating factor 1 / Caspase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHu, Q. / Wu, D. / Yan, C. / Shi, Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Molecular determinants of caspase-9 activation by the Apaf-1 apoptosome.
Authors: Hu, Q. / Wu, D. / Chen, W. / Yan, Z. / Yan, C. / He, T. / Liang, Q. / Shi, Y.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptotic protease-activating factor 1
B: Apoptotic protease-activating factor 1
C: Apoptotic protease-activating factor 1
D: Apoptotic protease-activating factor 1
E: Caspase-9
F: Caspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,62515
Polymers69,8826
Non-polymers7439
Water6,395355
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-150 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.531, 92.520, 68.031
Angle α, β, γ (deg.)90.00, 109.12, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHOR STATED THE BIOLOGICAL UNIT CONTAINS 7 APAF-1 CARDS AND 4 CASPASE-9 CARDS. BASED ON THEIR EXPERIMENTAL RESULTS, APAF-1 FORMS A HEPTAMER IN THE APOPTOSOME, AND IN THE HOLOENZYME FORMED BY THE APOPTOSOME AND CASPASE-9, THE MOLAR RATIO BETWEEN APAF-1 AND CASPASE-9 IS 7:4. HOWEVER, FURTHER VALIDATION IS REQUIRED.

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Components

#1: Protein
Apoptotic protease-activating factor 1 / APAF-1


Mass: 11099.710 Da / Num. of mol.: 4 / Fragment: card domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APAF1, KIAA0413 / Production host: Escherichia coli (E. coli) / References: UniProt: O14727
#2: Protein Caspase-9 / / CASP-9 / Apoptotic protease Mch-6 / Apoptotic protease-activating factor 3 / APAF-3 / ICE-like ...CASP-9 / Apoptotic protease Mch-6 / Apoptotic protease-activating factor 3 / APAF-3 / ICE-like apoptotic protease 6 / ICE-LAP6 / Caspase-9 subunit p35 / Caspase-9 subunit p10


Mass: 12741.549 Da / Num. of mol.: 2 / Fragment: card domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP9, MCH6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55211, caspase-9
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 13% PEG 3000, 0.2M ammonium sulfate, 0.1M MES (pH5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 44040 / Num. obs: 43908 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.18 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3YGS

3ygs


Resolution: 2.1→23.774 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2050 5.09 %RANDOM
Rwork0.2104 ---
all0.2113 44099 --
obs0.2113 40293 91.37 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.32 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1002 Å2-0 Å24.4189 Å2
2---0.9783 Å20 Å2
3----1.1219 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 37 355 4954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134672
X-RAY DIFFRACTIONf_angle_d1.1236274
X-RAY DIFFRACTIONf_dihedral_angle_d18.6581822
X-RAY DIFFRACTIONf_chiral_restr0.1694
X-RAY DIFFRACTIONf_plane_restr0.006814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.1490.31981220.221240786
2.149-2.20270.23371390.2135249490
2.2027-2.26220.27931360.2115242388
2.2622-2.32870.25271410.2127252091
2.3287-2.40380.26211330.2097249389
2.4038-2.48960.20471350.2082244989
2.4896-2.58920.26511110.2256249889
2.5892-2.70690.2731240.2275245888
2.7069-2.84940.24621030.2143253690
2.8494-3.02750.22651430.2165249690
3.0275-3.26080.23161500.2068260193
3.2608-3.58790.18131540.1953268996
3.5879-4.10480.18351460.19482782100
4.1048-5.16290.18881630.1928270297
5.1629-23.77550.27681500.2438269595
Refinement TLS params.Method: refined / Origin x: -16.1075 Å / Origin y: -22.2377 Å / Origin z: -0.0985 Å
111213212223313233
T-0.0182 Å20.0306 Å2-0.0049 Å2-0.0493 Å20.0115 Å2--0.0689 Å2
L0.0309 °20.0191 °2-0.1101 °2-0.1103 °2-0.017 °2--0.3105 °2
S-0.0887 Å °0.0561 Å °0.0054 Å °-0.0826 Å °0.1692 Å °0.195 Å °-0.0058 Å °-0.2011 Å °0.0228 Å °
Refinement TLS groupSelection details: all

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